Using histochemical methods offering high topographical resolution for evaluation of changes in the ischemic focus and the penumbra, the mitochondrial electron transport chain (ETC) complexes I, II, and IV were examined in rats subjected to 2 h of proximal occlusion of the middle cerebral artery (MCAO) followed by no reperfusion, 1 h reperfusion, 4 h reperfusion, or 4 h reperfusion plus treatment with the free radical scavenger alpha-PBN. Serial brain cryosections were histochemically stained to visualize activity of complexes I, II, and IV, and the volumes of tissue with reduced activity in the ipsilateral cortex and caudate putamen were measured by densitometric image analysis. Reductions in complex I, II, and IV activity were restricted to areas in the ischemic foci in cortex and caudate putamen, which microscopically displayed signs of early morphological damage. In cortex, the tissue volume with reduced activity did not change significantly during reperfusion but progressively increased in the caudate putamen, possibly reflecting a faster maturation of morphological damage in this region. Treatment with alpha-PBN did not affect the observed reductions in activities. We deduce that inhibition of mitochondrial ETC complex activity does not play a critical role for recruitment of the penumbra in the infarction process.